Chapter 8 Differential abundance analysis

8.1 CC acclimation vs post2

8.1.1 Enrichment analysis: Ancombc2

8.1.1.1 Structural zeros

# A tibble: 181 × 14
# Rowwise: 
   genome                present average domain      phylum               class                  order                 family              genus             species completeness contamination  length    gc
   <chr>                 <chr>     <dbl> <chr>       <chr>                <chr>                  <chr>                 <chr>               <chr>             <chr>          <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_11:bin_000008 accli     6.79  d__Bacteria p__Verrucomicrobiota c__Verrucomicrobiae    o__Verrucomicrobiales f__Akkermansiaceae  g__Akkermansia    s__            100            0.12 3054831  0.58
 2 AH1_2nd_1:bin_000039  accli     5.96  d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Bacteroidales      f__Marinifilaceae   g__Odoribacter    s__             99.5          0.1  3918820  0.44
 3 AH1_2nd_17:bin_000010 accli     2.61  d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Bacteroidales      f__Rikenellaceae    g__Mucinivorans   s__             98.1          0.06 2365004  0.44
 4 AH1_2nd_17:bin_000038 accli     2.42  d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Bacteroidales      f__Bacteroidaceae   g__Bacteroides_G  s__             88.0          3.29 4258067  0.4 
 5 AH1_2nd_14:bin_000005 accli     2.19  d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__Lachnospiraceae  g__               s__             97.1          0.82 3930509  0.3 
 6 AH1_2nd_5:bin_000002  accli     1.63  d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Bacteroidales      f__Marinifilaceae   g__Odoribacter    s__             99.6          0.04 3603552  0.45
 7 AH1_2nd_12:bin_000015 accli     1.52  d__Bacteria p__Bacillota         c__Bacilli             o__Erysipelotrichales f__Coprobacillaceae g__Thomasclavelia s__            100            7.76 3794096  0.31
 8 AH1_2nd_8:bin_000020  accli     1.25  d__Bacteria p__Pseudomonadota    c__Alphaproteobacteria o__RUG11792           f__RUG11792         g__               s__             99.6          0     892810  0.36
 9 AH1_2nd_1:bin_000028  accli     1.15  d__Bacteria p__Pseudomonadota    c__Alphaproteobacteria o__Rickettsiales      f__UBA1997          g__CALXRO01       s__             98.0          0     935376  0.28
10 AH1_2nd_12:bin_000063 accli     0.911 d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__Lachnospiraceae  g__CHH4-2         s__             72.2          2.05 3506133  0.42
# ℹ 171 more rows

8.1.1.2 MAG level

8.2 CC acclimation vs post1

8.2.1 Enrichment analysis: Ancombc2

8.2.1.1 Structural zeros

# A tibble: 206 × 14
# Rowwise: 
   genome                present average domain      phylum               class               order                 family                 genus            species completeness contamination  length    gc
   <chr>                 <chr>     <dbl> <chr>       <chr>                <chr>               <chr>                 <chr>                  <chr>            <chr>          <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_1:bin_000006  accli     13.1  d__Bacteria p__Bacillota_A       c__Clostridia       o__Lachnospirales     f__Lachnospiraceae     g__Kineothrix    s__             98.5          4.38 4263353  0.44
 2 AH1_2nd_18:bin_000011 accli     10.1  d__Bacteria p__Bacillota         c__Bacilli          o__Erysipelotrichales f__Coprobacillaceae    g__Coprobacillus s__             98.4          7.24 3675733  0.3 
 3 AH1_2nd_11:bin_000008 accli      6.79 d__Bacteria p__Verrucomicrobiota c__Verrucomicrobiae o__Verrucomicrobiales f__Akkermansiaceae     g__Akkermansia   s__            100            0.12 3054831  0.58
 4 AH1_2nd_17:bin_000023 accli      6.31 d__Bacteria p__Bacillota         c__Bacilli          o__Erysipelotrichales f__Coprobacillaceae    g__Coprobacillus s__             90.2          1.72 3372832  0.31
 5 LI1_2nd_4:bin_000026  accli      6.09 d__Bacteria p__Bacteroidota      c__Bacteroidia      o__Bacteroidales      f__Marinifilaceae      g__Odoribacter   s__             99.4          3.28 4761273  0.44
 6 AH1_2nd_1:bin_000039  accli      5.96 d__Bacteria p__Bacteroidota      c__Bacteroidia      o__Bacteroidales      f__Marinifilaceae      g__Odoribacter   s__             99.5          0.1  3918820  0.44
 7 AH1_2nd_17:bin_000010 accli      2.61 d__Bacteria p__Bacteroidota      c__Bacteroidia      o__Bacteroidales      f__Rikenellaceae       g__Mucinivorans  s__             98.1          0.06 2365004  0.44
 8 AH1_2nd_17:bin_000038 accli      2.42 d__Bacteria p__Bacteroidota      c__Bacteroidia      o__Bacteroidales      f__Bacteroidaceae      g__Bacteroides_G s__             88.0          3.29 4258067  0.4 
 9 AH1_2nd_20:bin_000016 accli      2.27 d__Bacteria p__Bacillota         c__Bacilli          o__Erysipelotrichales f__Erysipelotrichaceae g__              s__             97.5          3.86 4005468  0.37
10 AH1_2nd_14:bin_000005 accli      2.19 d__Bacteria p__Bacillota_A       c__Clostridia       o__Lachnospirales     f__Lachnospiraceae     g__              s__             97.1          0.82 3930509  0.3 
# ℹ 196 more rows

8.2.1.2 MAG level

8.3 WC acclimation vs post2

8.3.1 Enrichment analysis: Ancombc2

8.3.1.1 Structural zeros

# A tibble: 134 × 14
# Rowwise: 
   genome                present average domain      phylum          class          order                 family               genus               species                    completeness contamination  length    gc
   <chr>                 <chr>     <dbl> <chr>       <chr>           <chr>          <chr>                 <chr>                <chr>               <chr>                             <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_13:bin_000004 accli      2.13 d__Bacteria p__Bacillota_A  c__Clostridia  o__Lachnospirales     f__Lachnospiraceae   g__                 s__                                97.0          0.58 3761779  0.42
 2 LI1_2nd_2:bin_000048  accli      2.07 d__Bacteria p__Bacillota    c__Bacilli     o__Erysipelotrichales f__Coprobacillaceae  g__Coprobacillus    s__                                86.9          4.89 3159306  0.31
 3 AH1_2nd_12:bin_000008 accli      1.99 d__Bacteria p__Bacillota    c__Bacilli     o__Lactobacillales    f__Streptococcaceae  g__Lactococcus      s__Lactococcus formosensis         99.9          0.2  2049859  0.38
 4 LI1_2nd_3:bin_000015  accli      1.98 d__Bacteria p__Bacillota    c__Bacilli     o__Staphylococcales   f__Staphylococcaceae g__Staphylococcus   s__Staphylococcus shinii           91.7          3.54 2956427  0.32
 5 LI1_2nd_8:bin_000044  accli      1.47 d__Bacteria p__Bacillota_A  c__Clostridia  o__Oscillospirales    f__Ruminococcaceae   g__Angelakisella    s__                                80.1          3.35 2723215  0.62
 6 LI1_2nd_2:bin_000030  accli      1.14 d__Bacteria p__Bacillota    c__Bacilli     o__RF39               f__UBA660            g__Caccenecus       s__                                91.6          1.86 1128677  0.28
 7 LI1_2nd_2:bin_000002  accli      1.10 d__Bacteria p__Bacillota_A  c__Clostridia  o__Oscillospirales    f__Ruminococcaceae   g__Ruthenibacterium s__                                94.7          2.65 2840729  0.53
 8 AH1_2nd_6:bin_000006  accli      1.09 d__Bacteria p__Bacillota_A  c__Clostridia  o__Lachnospirales     f__Lachnospiraceae   g__JAAYNV01         s__                                99.8          0.57 3690498  0.45
 9 LI1_2nd_1:bin_000052  accli      1.07 d__Bacteria p__Bacillota_A  c__Clostridia  o__TANB77             f__CAG-508           g__RGIG8482         s__                                83.8          7.54 1933783  0.3 
10 AH1_2nd_16:bin_000045 accli      1.07 d__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales      f__Rikenellaceae     g__Alistipes        s__                                93.6          6.68 3445818  0.59
# ℹ 124 more rows

8.3.1.2 MAG level

8.4 CI acclimation vs post2

8.4.1 Enrichment analysis: Ancombc2

8.4.1.1 Structural zeros

# A tibble: 195 × 14
# Rowwise: 
   genome                present average domain      phylum          class          order                 family                 genus                species completeness contamination  length    gc
   <chr>                 <chr>     <dbl> <chr>       <chr>           <chr>          <chr>                 <chr>                  <chr>                <chr>          <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_1:bin_000006  accli     39.3  d__Bacteria p__Bacillota_A  c__Clostridia  o__Lachnospirales     f__Lachnospiraceae     g__Kineothrix        s__             98.5          4.38 4263353  0.44
 2 LI1_2nd_7:bin_000008  accli      7.37 d__Bacteria p__Bacillota    c__Bacilli     o__Erysipelotrichales f__Erysipelotrichaceae g__Breznakia         s__             97.9          2.36 2618172  0.3 
 3 AH1_2nd_18:bin_000013 accli      4.35 d__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales      f__Tannerellaceae      g__Parabacteroides   s__             98.7          0.01 4005076  0.43
 4 AH1_2nd_20:bin_000004 accli      2.87 d__Bacteria p__Bacillota_A  c__Clostridia  o__Lachnospirales     f__Lachnospiraceae     g__Roseburia         s__            100.           0.43 3729496  0.42
 5 AH1_2nd_5:bin_000054  accli      2.45 d__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales      f__Bacteroidaceae      g__Bacteroides       s__             86.4          3.24 5336241  0.43
 6 AH1_2nd_1:bin_000001  accli      1.71 d__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales      f__Tannerellaceae      g__Parabacteroides_B s__             99.6          1.94 4534617  0.51
 7 AH1_2nd_20:bin_000061 accli      1.69 d__Bacteria p__Bacillota    c__Bacilli     o__Lactobacillales    f__Enterococcaceae     g__Enterococcus      s__             92.6          6.02 4153944  0.4 
 8 AH1_2nd_16:bin_000008 accli      1.59 d__Bacteria p__Bacillota_A  c__Clostridia  o__Lachnospirales     f__                    g__                  s__             98.4          0.14 3874322  0.28
 9 LI1_2nd_3:bin_000007  accli      1.48 d__Bacteria p__Bacillota    c__Bacilli     o__Erysipelotrichales f__Erysipelotrichaceae g__C-19              s__             99.8          1.24 3665262  0.36
10 AH1_2nd_10:bin_000044 accli      1.20 d__Bacteria p__Bacillota_A  c__Clostridia  o__Lachnospirales     f__Lachnospiraceae     g__Enterocloster     s__             88.9          0.53 3623272  0.48
# ℹ 185 more rows

8.4.1.2 MAG level

8.5 CI acclimation vs post1

8.5.1 Enrichment analysis: Ancombc2

8.5.1.1 Structural zeros

# A tibble: 223 × 14
# Rowwise: 
   genome                present average domain      phylum               class                  order                 family                 genus              species completeness contamination  length    gc
   <chr>                 <chr>     <dbl> <chr>       <chr>                <chr>                  <chr>                 <chr>                  <chr>              <chr>          <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_1:bin_000006  accli     39.3  d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__Lachnospiraceae     g__Kineothrix      s__             98.5          4.38 4263353  0.44
 2 AH1_2nd_19:bin_000005 accli     24.7  d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__Lachnospiraceae     g__Roseburia       s__             96.1          0.16 3941649  0.42
 3 AH1_2nd_13:bin_000004 accli     11.5  d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__Lachnospiraceae     g__                s__             97.0          0.58 3761779  0.42
 4 AH1_2nd_11:bin_000008 accli      9.27 d__Bacteria p__Verrucomicrobiota c__Verrucomicrobiae    o__Verrucomicrobiales f__Akkermansiaceae     g__Akkermansia     s__            100            0.12 3054831  0.58
 5 AH1_2nd_19:bin_000001 accli      8.34 d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Bacteroidales      f__Tannerellaceae      g__Parabacteroides s__             99.7          1.43 4736923  0.51
 6 AH1_2nd_19:bin_000038 accli      8.08 d__Bacteria p__Pseudomonadota    c__Alphaproteobacteria o__RUG11792           f__                    g__                s__             94.6          0     932470  0.37
 7 LI1_2nd_7:bin_000008  accli      7.37 d__Bacteria p__Bacillota         c__Bacilli             o__Erysipelotrichales f__Erysipelotrichaceae g__Breznakia       s__             97.9          2.36 2618172  0.3 
 8 AH1_2nd_18:bin_000047 accli      6.98 d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Bacteroidales      f__Tannerellaceae      g__Parabacteroides s__             87.5          4.81 5473283  0.43
 9 AH1_2nd_9:bin_000015  accli      6.88 d__Bacteria p__Desulfobacterota  c__Desulfovibrionia    o__Desulfovibrionales f__Desulfovibrionaceae g__Desulfovibrio   s__             99.0          0    3043039  0.61
10 AH1_2nd_10:bin_000007 accli      6.07 d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__                    g__                s__             97.5          0.68 3552238  0.29
# ℹ 213 more rows

8.5.1.2 MAG level

8.6 post2 CC and CI

8.6.1 Enrichment analysis: Ancombc2

8.6.1.1 Structural zeros

# A tibble: 174 × 14
# Rowwise: 
   genome                present  average domain      phylum             class                  order                  family                  genus                species completeness contamination  length    gc
   <chr>                 <chr>      <dbl> <chr>       <chr>              <chr>                  <chr>                  <chr>                   <chr>                <chr>          <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_18:bin_000013 cc_post2   36.2  d__Bacteria p__Bacteroidota    c__Bacteroidia         o__Bacteroidales       f__Tannerellaceae       g__Parabacteroides   s__             98.7          0.01 4005076  0.43
 2 AH1_2nd_15:bin_000002 cc_post2    7.12 d__Bacteria p__Cyanobacteriota c__Vampirovibrionia    o__Gastranaerophilales f__Gastranaerophilaceae g__Limenecus         s__             99.8          0.87 2111746  0.37
 3 LI1_2nd_7:bin_000001  cc_post2    4.42 d__Bacteria p__Bacillota_A     c__Clostridia          o__Clostridiales       f__Clostridiaceae       g__Sarcina           s__             98.3          1.37 3938038  0.28
 4 AH1_2nd_9:bin_000061  cc_post2    4.33 d__Bacteria p__Pseudomonadota  c__Gammaproteobacteria o__Burkholderiales     f__Burkholderiaceae_C   g__Alcaligenes       s__             72.8          6.01 3338181  0.57
 5 AH1_2nd_7:bin_000015  cc_post2    3.75 d__Bacteria p__Pseudomonadota  c__Alphaproteobacteria o__RF32                f__CAG-239              g__CAZU01            s__            100            0.49 1794016  0.43
 6 AH1_2nd_1:bin_000001  cc_post2    2.77 d__Bacteria p__Bacteroidota    c__Bacteroidia         o__Bacteroidales       f__Tannerellaceae       g__Parabacteroides_B s__             99.6          1.94 4534617  0.51
 7 AH1_2nd_7:bin_000006  cc_post2    1.87 d__Bacteria p__Bacillota_A     c__Clostridia          o__Lachnospirales      f__Lachnospiraceae      g__JALFVM01          s__            100            2.39 4970285  0.43
 8 AH1_2nd_7:bin_000065  cc_post2    1.49 d__Bacteria p__Bacteroidota    c__Bacteroidia         o__Bacteroidales       f__Tannerellaceae       g__Parabacteroides   s__             93.7          2.1  5263338  0.43
 9 AH1_2nd_7:bin_000038  cc_post2    1.47 d__Bacteria p__Bacillota_A     c__Clostridia          o__Oscillospirales     f__Ruminococcaceae      g__                  s__             91.7          4.31 2931073  0.49
10 AH1_2nd_19:bin_000017 cc_post2    1.35 d__Bacteria p__Bacillota_A     c__Clostridia          o__Lachnospirales      f__Lachnospiraceae      g__Caccomorpha       s__             92.8          4.49 5611813  0.47
# ℹ 164 more rows

8.6.1.2 MAG level

8.7 post2 WC and CI

8.7.1 Enrichment analysis: Ancombc2

####Structural zeros

# A tibble: 161 × 14
# Rowwise: 
   genome                present  average domain      phylum               class                  order                 family                 genus                   species completeness contamination  length    gc
   <chr>                 <chr>      <dbl> <chr>       <chr>                <chr>                  <chr>                 <chr>                  <chr>                   <chr>          <dbl>         <dbl>   <dbl> <dbl>
 1 AH1_2nd_14:bin_000015 ci_post2   17.8  d__Bacteria p__Bacillota_A       c__Clostridia          o__Christensenellales f__UBA3700             g__                     s__             94.8          0    2023163  0.36
 2 AH1_2nd_1:bin_000028  ci_post2    4.77 d__Bacteria p__Pseudomonadota    c__Alphaproteobacteria o__Rickettsiales      f__UBA1997             g__CALXRO01             s__             98.0          0     935376  0.28
 3 AH1_2nd_12:bin_000041 ci_post2    4.76 d__Bacteria p__Bacillota         c__Bacilli             o__Mycoplasmatales    f__Mycoplasmoidaceae   g__Mycoplasmoides       s__             92.6          0.18 1005235  0.27
 4 AH1_2nd_8:bin_000020  ci_post2    4.34 d__Bacteria p__Pseudomonadota    c__Alphaproteobacteria o__RUG11792           f__RUG11792            g__                     s__             99.6          0     892810  0.36
 5 AH1_2nd_1:bin_000015  ci_post2    4.10 d__Bacteria p__Bacillota_A       c__Clostridia          o__Lachnospirales     f__Lachnospiraceae     g__MGBC136627           s__             96.6          0.56 3882618  0.33
 6 AH1_2nd_19:bin_000052 ci_post2    3.95 d__Bacteria p__Verrucomicrobiota c__Verrucomicrobiae    o__Opitutales         f__LL51                g__                     s__             92.8          0     889473  0.53
 7 AH1_2nd_2:bin_000034  ci_post2    3.09 d__Bacteria p__Verrucomicrobiota c__Verrucomicrobiae    o__Opitutales         f__LL51                g__                     s__             93.8          0     862378  0.56
 8 AH1_2nd_6:bin_000001  ci_post2    2.21 d__Bacteria p__Bacteroidota      c__Bacteroidia         o__Flavobacteriales   f__Weeksellaceae       g__Moheibacter          s__             98.7          0.1  3381883  0.36
 9 AH1_2nd_10:bin_000009 ci_post2    1.72 d__Bacteria p__Desulfobacterota  c__Desulfovibrionia    o__Desulfovibrionales f__Desulfovibrionaceae g__Bilophila            s__             97.9          0.61 3772750  0.51
10 AH1_2nd_5:bin_000037  ci_post2    1.67 d__Bacteria p__Bacillota_A       c__Clostridia          o__Oscillospirales    f__Oscillospiraceae    g__Pseudoflavonifractor s__             93.4          7.74 3923478  0.58
# ℹ 151 more rows

8.7.1.1 MAG level

8.8 Community level plots

accli_post2<-sample_metadata%>% 
  filter(time_point == "1_Acclimation"|time_point == "6_Post-FMT2")
accli_post2$newID<-paste(accli_post2$type, "_", accli_post2$time_point)

GIFTs_functions_community %>%
  as.data.frame() %>%
  rownames_to_column("sample") %>%
  left_join(accli_post2, by = join_by(sample == Tube_code)) %>%
  filter(time_point == "1_Acclimation"|time_point == "6_Post-FMT2") %>%
  select(c(1:29, 36,39)) %>%
  pivot_longer(-c(sample,type,time_point),names_to = "trait", values_to = "value") %>%
  mutate(trait = case_when(
    trait %in% GIFT_db3$Code_function ~ GIFT_db3$Function[match(trait, GIFT_db3$Code_function)],
    TRUE ~ trait
  )) %>%
  mutate(trait=factor(trait,levels=unique(GIFT_db3$Function))) %>%
  ggplot(aes(x=value, y=time_point, group=time_point, fill=type, color=type)) +
  geom_boxplot() +
  scale_color_manual(name="type",
                     breaks=c("Control","Hot_control", "Treatment"),
                     labels=c("Cold-Cold","Hot-Hot", "Cold-Hot"),
                     values=c("#4477AA","#d57d2c","#76b183")) +
  scale_fill_manual(name="type",
                    breaks=c("Control","Hot_control", "Treatment"),
                    labels=c("Cold-Cold","Hot-Hot", "Cold-Hot"),
                    values=c("#4477AA50","#d57d2c50","#76b18350")) +
  facet_grid(trait ~ type, space="free", scales="free") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
        strip.text.y = element_text(angle = 0)) + 
  labs(y="Traits",x="Metabolic capacity index")

GIFTs_elements_community_merged<-GIFTs_elements_community %>%
    as.data.frame() %>%
    rownames_to_column(var="sample") %>%
    filter(sample!="AD69") %>%
    pivot_longer(!sample,names_to="trait",values_to="gift") %>%
    left_join(sample_metadata, by = join_by(sample == Tube_code))%>%
    filter(time_point=="1_Acclimation"|time_point == "6_Post-FMT2")%>%
    mutate(functionid = substr(trait, 1, 3)) %>%
    mutate(trait = case_when(
      trait %in% GIFT_db3$Code_element ~ GIFT_db3$Element[match(trait, GIFT_db3$Code_element)],
      TRUE ~ trait
    )) %>%
    mutate(functionid = case_when(
      functionid %in% GIFT_db3$Code_function ~ GIFT_db3$Function[match(functionid, GIFT_db3$Code_function)],
      TRUE ~ functionid
    )) %>%
    mutate(trait=factor(trait,levels=unique(GIFT_db3$Element))) %>%
    mutate(functionid=factor(functionid,levels=unique(GIFT_db3$Function)))

# Create an interaction variable for time_point and sample
GIFTs_elements_community_merged$interaction_var <- interaction(GIFTs_elements_community_merged$sample, GIFTs_elements_community_merged$time_point)
  
ggplot(GIFTs_elements_community_merged,aes(x=interaction_var,y=trait,fill=gift)) +
        geom_tile(colour="white", linewidth=0.2)+
        scale_fill_gradientn(colours=rev(c("#d53e4f", "#f46d43", "#fdae61", "#fee08b", "#e6f598", "#abdda4", "#ddf1da")))+
        facet_grid(functionid ~ type, scales="free",space="free") +
        theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1, size=5),
              strip.text.y = element_text(angle = 0)) + 
        labs(y="Traits",x="Time_point",fill="GIFT")+
  scale_x_discrete(labels = function(x) gsub(".*\\.", "", x))

8.9 Wilcoxon comparison

8.9.1 Community elements differences: in CC acclimation vs post2

difference_table_CC %>% 
  filter(group_color=="Acclimation")
  Elements Acclimation      Post2                      Function     Element Difference group_color
1    T0503   0.1830714 0.01253516 Vitamin transport_Niacin (B3) Niacin (B3)  0.1705362 Acclimation

8.9.2 Community elements differences: in CI acclimation vs post2

difference_table_CI %>% 
  filter(group_color=="Acclimation")

8.9.3 Community elements differences: in WC acclimation vs post2

difference_table_WC %>% 
  filter(group_color=="Acclimation")

8.9.4 Comparison of both population in wild samples

difference_table_WC %>% 
  filter(group_color=="Acclimation")
  Elements Acclimation      Post2                              Function          Element Difference group_color
1    T0211  0.07898304 0.03960845           Amino acid transport_Serine           Serine 0.03937459 Acclimation
2    T0705  0.03026609 0.01792140      Nucleic acid transport_Allantoin        Allantoin 0.01234469 Acclimation
3    T0401  0.08571001 0.03355773    Organic anion transport_Spermidine       Spermidine 0.05215228 Acclimation
4    T0406  0.06660075 0.02039130     Organic anion transport_Succinate        Succinate 0.04620945 Acclimation
5    D0301  0.03445823 0.02175758             Sugar degradation_Lactose          Lactose 0.01270065 Acclimation
6    B0711  0.31689890 0.23431920 Vitamin biosynthesis_Menaquinone (K2) Menaquinone (K2) 0.08257970 Acclimation
7    T0503  0.05906234 0.02697581         Vitamin transport_Niacin (B3)      Niacin (B3) 0.03208653 Acclimation

####Butiryc acid biosynthesis

8.9.5 Comparison of both population in acclimation samples

8.9.6 Comparison of CC and CI in post2 samples

8.9.7 Comparison of CI and WC in post2 samples

8.9.8 Comparison of CI in accli and post1 samples

8.9.9 Comparison of CC in accli and post1 samples